Distinct genetic determinants and mechanisms of SARS-CoV-2 resistance to remdesivir

Stevens, L. J.; Pruijssers, A. J.; Lee, H. W.; Gordon, C. J.; Tchesnokov, E. P.; Gribble, J.; George, A. S.; Hughes, T. M.; Lu, X.; Li, J.; Perry, J. K.; Porter, D. P.; Cihlar, T.; Sheahan, T. P.; Baric, R. S.; Gotte, M.; Denison, M. R.

doi:10.1101/2022.01.25.477724

bioRxiv · 10.1101/2022.01.25.477724

Distinct genetic determinants and mechanisms of SARS-CoV-2 resistance to remdesivir

Stevens, L. J.·Pruijssers, A. J.·Lee, H. W.·Gordon, C. J.·Tchesnokov, E. P.·Gribble, J.·George, A. S.·Hughes, T. M.·Lu, X.·Li, J.·Perry, J. K.·Porter, D. P.·Cihlar, T.·Sheahan, T. P.·Baric, R. S.·Gotte, M.·Denison, M. R.

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Abstract

The nucleoside analog remdesivir (RDV) is an FDA-approved antiviral for the treatment of SARS- CoV-2 infections, and as such it is critical to understand potential genetic determinants and barriers to RDV resistance. In this study, SARS-CoV-2 was subjected to 13 passages in cell culture with increasing concentrations of GS-441524, the parent nucleoside of RDV. At passage 13 the RDV resistance of the lineages ranged from 2.7-to 10.4-fold increase in EC50. Sequence analysis of the three lineage populations identified non-synonymous mutations in the nonstructural protein 12 RNA-dependent RNA polymerase (nsp12-RdRp): V166A, N198S, S759A, V792I and C799F/R. Two of the three lineages encoded the S759A substitution at the RdRp Ser759-Asp-Asp active motif. In one lineage, the V792I substitution emerged first then combined with S759A. Introduction of the S759A and V792I substitutions at homologous nsp12 positions in viable isogenic clones of the betacoronavirus murine hepatitis virus (MHV) demonstrated their transferability across CoVs, up to 38-fold RDV resistance in combination, and a significant replication defect associated with their introduction. Biochemical analysis of SARS-CoV-2 RdRp encoding S759A demonstrated a [~]10- fold decreased preference for RDV-triphosphate (RDV-TP) as a substrate, while nsp12-V792I diminished the UTP concentration needed to overcome the template-dependent inhibition associated with RDV. The in vitro selected substitutions here identified were rare or not detected in the >6 million publicly available nsp12-RdRp consensus sequences in the absence of RDV selection. The results define genetic and biochemical pathways to RDV resistance and emphasize the need for additional studies to define the potential for emergence of these or other RDV resistance mutations in various clinical settings. One Sentence SummarySARS-CoV-2 develops in vitro resistance to remdesivir by distinct and complementary mutations and mechanisms in the viral polymerase

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Stevens, L. J., Pruijssers, A. J., Lee, H. W., Gordon, C. J., Tchesnokov, E. P., Gribble, J., George, A. S., Hughes, T. M., Lu, X., Li, J., Perry, J. K., Porter, D. P., Cihlar, T., Sheahan, T. P., Baric, R. S., Gotte, M., Denison, M. R.. 2022-01-29. Distinct genetic determinants and mechanisms of SARS-CoV-2 resistance to remdesivir. https://doi.org/10.1101/2022.01.25.477724

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